You're right. I think Lex being responsible for the creation of Metallo is an interesting angle.

If they wanted to really save Brainiac for a third film (which I wouldn't be up for personally at the moment)..then they could always go with this scenario:

MOS would introduce villains in the form of Zod and Faora to show the worst that Krypton had to offer, and the sequel would show the worst that Earth had to offer in the evil deeds and acts that came from Lex's actions.

Hell, throw in the suicide squad, or superman revenge team; essentially earth based villains, or a group that's comparable to Spider-Man's Sinister 6 Line up...and have them all try to take down Superman under Lex's orders....